| Class | Description |
|---|---|
| AlleleBiasedDownsamplingUtils |
The purpose of this set of utilities is to downsample a set of reads to remove contamination.
|
| Downsampler<T> |
The basic downsampler API, with no reads-specific operations.
|
| DownsamplingMethod |
Describes the method for downsampling reads at a given locus.
|
| FractionalDownsampler |
Fractional Downsampler: selects a specified fraction of the reads for inclusion.
|
| LevelingDownsampler<T extends java.util.List<E>,E> |
Leveling Downsampler: Given a set of Lists of arbitrary items and a target size, removes items from
the Lists in an even fashion until the total size of all Lists is <= the target size.
|
| MutectDownsampler | |
| PassThroughDownsampler |
Pass-Through Downsampler: Implementation of the ReadsDownsampler interface that does no
downsampling whatsoever, and instead simply "passes-through" all the reads it's given.
|
| PositionalDownsampler |
PositionalDownsampler: Downsample each stack of reads at each alignment start to a size <= a target coverage
using a
ReservoirDownsampler. |
| ReadsDownsampler |
An extension of the basic downsampler API with reads-specific operations
|
| ReadsDownsamplingIterator |
Iterator wrapper around our generic
ReadsDownsampler) interface. |
| ReservoirDownsampler |
Reservoir Downsampler: Selects n reads out of a stream whose size is not known in advance, with
every read in the stream having an equal chance of being selected for inclusion.
|
| Enum | Description |
|---|---|
| DownsampleType |
Type of downsampling method to invoke.
|